How can I annotate human genomic intervals (BED file) from a ChIP-seq experiment with information such as whether the interval overlaps with a gene(s)? Upstream of a gene? Overlaps with an exon? Intron? 5kb upstream/downstream of TSS? Intergenic? Does it overlap with a DNAse I hypersensitive site?
Surely bedtools can help me with this, but I'm looking for the best workflow / data sources to use for this that will require the least amount of scripting.
Thanks.